It would seem that different branches of the Dark Brotherhood seem to worship different night mothers, a number of them mortal. Perhaps Mephala pulls the strings behind the Cyrodiilic version, but the branches in Morrowind and Hammerfell had human night mothers, seemingly having no further connection to Mephala.
Edit: http://www.uesp.net/wiki/Oblivion:Sacred_Witness seems to suggest that the belief in Mephala worship was around in Hammerfell, I suspect they moved away from Mephala worship somewhere along the line.
The mortal ones are, for the most part, titles. Some of them know that they aren't the real Night Mother, some of them might even be acting on Mephala's orders, but a small portion of them are probably heretics. They declare themselves the real Night Mother reborn and start a new sect, I imagine the Brotherhood isn't as centralized as we think. It's my guess that each province's DB is independent, though I would guess they collaborate to some degree.
Ah, that text is an interesting one, and a decent theory, to say the least. It is a piece of the puzzle, a biased account, and conflicts with the others as much as they do with it. In the end we can't say for certain, but a meshing of these texts might be best.
So, that text tells us that one of the Brotherhoods, in Hammerfell, was created by or at least led by this ex-Thieve's Guild member. Plausible enough. But we also have text to prove that the Brotherhood split off from the Tong, led by the Night Mother, because of financial and religious reasons. However, at the same time, some texts claim that the Night Mother was a title of the Tong as well.
My favorite source is this one, from http://www.imperial-library.info/mwbooks/brothers_of_darkness.shtml:
The Dark Brotherhood sprang from a religious order, the Morag Tong, during the Second Era. The Morag Tong were worshippers of the Daedra spirit Mephala, who encouraged them to commit ritual murders. In their early years, they were as disorganized as only obscure cultists could be-there was no one to lead the band, and as a group they dared not murder anybody of any importance. This changed with the rise of the Night Mother.
All leaders of the Morag Tong, and then afterward the Dark Brotherhood, have been called the Night Mother. Whether the same woman (if it is even a woman) has commanded the Dark Brotherhood since the Second Era is unknown. What is believed is that the original Night Mother developed an important doctrine of the Morag Tong-the belief that, while Mephala does grow stronger with every murder committed in her name, certain murders were better than others. Murders that came from hate pleased Mephala more than murders committed because of greed. Murders of great men and women pleased Mephala more than murders of relative unknowns.
So, it is said that the title of Night Mother was one of a mortal, something to be passed down from person to person. However, whether these individuals were in some way controlled or in contact with Mephala is unclear. What is certain is that they could not hope to get contracts from secret prayers and rituals all the way to the mortal Night Mother, unless these rituals used some form of alchemical magic. What is also certain is that the ghost we see in Oblivion (while Oblivion may not be the best source) was no mere mortal. Thus my theory of her being both a title and Mephala stands.
We can approximate the time this belief was adopted with the first known murder committed by the Morag Tong. In the year 324 of the Second Era, the Potentate Versidue-Shaie was murdered in his palace in what is today the Elsweyr kingdom of Senchal. In a brash move, the Night Mother announced the identity of the murderers by painting "MORAG TONG" on the walls in the Potentate's own blood.
Previous to that, the Morag Tong existed in relative peace, more or less like a witches' coven-occasionally persecuted but usually ignored. In remarkable synchronicity at a time when Tamriel the Arena was a fractured land, the Morag Tong was outlawed throughout the continent. Every sovereign gave the cult's elimination his highest priority. Nothing more was officially heard of them for a hundred years.
This is when they retreated the Morrowind and appealed to Vivec. Thus when strife would arise and the schism would occur, the Night Mother leader taking her loyalist assassins and forming the Brotherhood, who wanted both money and religious freedom (No Vehk).
It is more difficult to date the Era when the Morag Tong re-emerged as the Dark Brotherhood, especially as other guilds of assassins have sporadically appeared throughout the history of Tamriel. The first mention of the Dark Brotherhood that I have found is from the journals of the Blood Queen Arlimahera of Hegathe. She spoke of slaying her enemies by her own hand, or if necessary "with the help of the Night Mother and her Dark Brotherhood, the secret arsenal my family has employed since my grandfather's time." Arlimahera wrote this in 2E412, so one can surmise that the Dark Brotherhood had been in existence since at least 360 if her grandfather had truly made use of them.
Only about thirty years since the Potentate assassination. The dates match up well, no?
So, it is my personal belief that Mephala is the driving religious force behind both organizations, though she may not control them directly. A "Night Mother" exists, at least in name, in each group or sect, the equivelant of the Tong's Grandmaster. The Listener is a Cyrodiil only thing, as their Night Mother is literally Mephala, controlling them from her statue. Notice that Daggerfall had no Listener rank
So you have to think about each sect individually, especially concerning the Night Mother.